1
|
Khalilollah S, Kalantari Soltanieh S, Obaid Saleh R, Ali Alzahrani A, Ghaleb Maabreh H, Mazin Al-Hamdani M, Dehghani-Ghorbi M, Shafiei Khonachaei M, Akhavan-Sigari R. LncRNAs involvement in pathogenesis of immune-related disease via regulation of T regulatory cells, an updated review. Cytokine 2024; 179:156585. [PMID: 38579428 DOI: 10.1016/j.cyto.2024.156585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 03/03/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024]
Abstract
The pathophysiology of several illnesses, including cancer and autoimmune diseasesdepends on human regulatory T cells (Tregs), and abnormalities in these cells may function as triggers for these conditions. Cancer and autoimmune, and gynecological diseases are associated with the differentiation of the proinflammatory T cell subset TH17 and its balance with the production of Treg. Recently, long non-coding RNAs (lncRNAs) have become important regulatory molecules in a wide range of illnesses. During epigenetic regulation, they can control the expression of important genes at several levels by affecting transcription, post-transcriptional actions, translation, and protein modification. They might connect with different molecules, such as proteins, DNA and RNA, and their structural composition is intricate. Because lncRNAs regulatebiological processes, including cell division, death, and growth, they are linked to severaldiseases. A notable instance of this is the lncRNA NEAT1, which has been the subject of several investigations to ascertain its function in immune cell development. In the context of immune cell development, several additional lncRNAs have been connected to Treg cell differentiation. In this work, we summarize current findings about the diverse functions of lncRNAs in Treg cell differentiation and control of the Th17/Treg homeostasis in autoimmune disorders, cancers, as well as several gynecological diseases where Tregs are key players.
Collapse
Affiliation(s)
- Shayan Khalilollah
- Department of Neurosurgery, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | | | - Raed Obaid Saleh
- Department of Pathological Analysis, College of Applied Science, University of Fallujah, Al-Anbar, Iraq.
| | | | - Hatem Ghaleb Maabreh
- Department of Dermatovenerology, Foreign Languages, RUDN University (Peoples' Friendship University of Russia named after Patrice Lumumba), Moscow, Russia.
| | | | - Mahmoud Dehghani-Ghorbi
- Hematology-Oncology Department, Imam Hossein Educational Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | | | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center, Tuebingen, Germany; Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Poland.
| |
Collapse
|
2
|
Tan RZ, Jia J, Li T, Wang L, Kantawong F. A systematic review of epigenetic interplay in kidney diseases: Crosstalk between long noncoding RNAs and methylation, acetylation of chromatin and histone. Biomed Pharmacother 2024; 176:116922. [PMID: 38870627 DOI: 10.1016/j.biopha.2024.116922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/06/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024] Open
Abstract
The intricate crosstalk between long noncoding RNAs (lncRNAs) and epigenetic modifications such as chromatin/histone methylation and acetylation offer new perspectives on the pathogenesis and treatment of kidney diseases. lncRNAs, a class of transcripts longer than 200 nucleotides with no protein-coding potential, are now recognized as key regulatory molecules influencing gene expression through diverse mechanisms. They modulate the epigenetic modifications by recruiting or blocking enzymes responsible for adding or removing methyl or acetyl groups, such as DNA, N6-methyladenosine (m6A) and histone methylation and acetylation, subsequently altering chromatin structure and accessibility. In kidney diseases such as acute kidney injury (AKI), chronic kidney disease (CKD), diabetic nephropathy (DN), glomerulonephritis (GN), and renal cell carcinoma (RCC), aberrant patterns of DNA/RNA/histone methylation and acetylation have been associated with disease onset and progression, revealing a complex interplay with lncRNA dynamics. Recent studies have highlighted how lncRNAs can impact renal pathology by affecting the expression and function of key genes involved in cell cycle control, fibrosis, and inflammatory responses. This review will separately address the roles of lncRNAs and epigenetic modifications in renal diseases, with a particular emphasis on elucidating the bidirectional regulatory effects and underlying mechanisms of lncRNAs in conjunction with DNA/RNA/histone methylation and acetylation, in addition to the potential exacerbating or renoprotective effects in renal pathologies. Understanding the reciprocal relationships between lncRNAs and epigenetic modifications will not only shed light on the molecular underpinnings of renal pathologies but also present new avenues for therapeutic interventions and biomarker development, advancing precision medicine in nephrology.
Collapse
Affiliation(s)
- Rui-Zhi Tan
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Jian Jia
- Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Tong Li
- Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Li Wang
- Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - Fahsai Kantawong
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand.
| |
Collapse
|
3
|
Feng W, Jiang Y, Zeng L, Ouyang Y, Li H, Tang Y, Luo L, Ouyang L, Xie L, Tan Y, Li Y. SPACA6P-AS: a trailblazer in breast cancer pathobiology and therapeutics. Cell Biol Toxicol 2024; 40:49. [PMID: 38922500 PMCID: PMC11208203 DOI: 10.1007/s10565-024-09870-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024]
Abstract
OBJECTIVE The primary objective of this investigation is to delve into the involvement of the long noncoding RNA (lncRNA) SPACA6P-AS in breast cancer (BC) development, focusing on its expression pattern, association with clinical-pathological features, impact on prognosis, as well as its molecular and immunological implications. METHODS Bioinformatics analysis was conducted utilizing RNA sequencing data of 1083 BC patients from the TCGA database. Functional exploration of SPACA6P-AS was carried out through the construction of survival curves, GO and KEGG enrichment analysis, and single-sample gene set enrichment analysis (ssGSEA). Furthermore, its functionality was validated through in vitro cell experiments and in vivo nude mouse model experiments. RESULTS SPACA6P-AS showed a remarkable increase in expression levels in BC tissues (p < 0.001) and demonstrated a close relationship to poor prognosis (overall survival HR = 1.616, progression-free interval HR = 1.40, disease-specific survival HR = 1.54). Enrichment analysis revealed that SPACA6P-AS could impact biological functions such as protease regulation, endopeptidase inhibitor activity, taste receptor activity, taste transduction, and maturity-onset diabetes of the young pathway. ssGSEA analysis indicated a negative correlation between SPACA6P-AS expression and immune cell infiltration like dendritic cells and neutrophils, while a positive correlation was observed with central memory T cells and T helper 2 cells. Results from in vitro and in vivo experiments illustrated that silencing SPACA6P-AS significantly inhibited the proliferation, migration, and invasion capabilities of BC cells. In vitro experiments also highlighted that dendritic cells with silenced SPACA6P-AS exhibited enhanced capabilities in promoting the proliferation of autologous CD3 + T cells and cytokine secretion. These discoveries elucidate the potential multifaceted roles of SPACA6P-AS in BC, including its potential involvement in modulating immune cell infiltration in the tumor microenvironment. CONCLUSION The high expression of lncRNA SPACA6P-AS in BC is closely linked to poor prognosis and may facilitate tumor progression by influencing specific biological processes, signaling pathways, and the immune microenvironment. The regulatory role of SPACA6P-AS positions it as a prospective biomarker and target for therapeutic approaches for BC diagnosis and intervention.
Collapse
Affiliation(s)
- Wenjie Feng
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Yiling Jiang
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Lijun Zeng
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Yuhan Ouyang
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Hailong Li
- Department of Pathology, Changde Hospital, Xiangya School of Medicine, Central South University, the First People's Hospital of Changde City, Changde, Hunan, People's Republic of China
| | - Yuanbin Tang
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Lunqi Luo
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Lianjie Ouyang
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China
| | - Liming Xie
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China.
| | - Yeru Tan
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China.
| | - Yuehua Li
- Department of Oncology, the First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, People's Republic of China.
| |
Collapse
|
4
|
Menon G, Mateo-Bonmati E, Reeck S, Maple R, Wu Z, Ietswaart R, Dean C, Howard M. Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing. Mol Cell 2024; 84:2255-2271.e9. [PMID: 38851186 DOI: 10.1016/j.molcel.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 06/10/2024]
Abstract
The mechanisms and timescales controlling de novo establishment of chromatin-mediated transcriptional silencing by Polycomb repressive complex 2 (PRC2) are unclear. Here, we investigate PRC2 silencing at Arabidopsis FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation activity, and PRC2 function, but so far not mechanistically connected. We develop and test a computational model describing proximal polyadenylation/termination mediated by the RNA-binding protein FCA that induces H3K4me1 removal by the histone demethylase FLD. H3K4me1 removal feeds back to reduce RNA polymerase II (RNA Pol II) processivity and thus enhance early termination, thereby repressing productive transcription. The model predicts that this transcription-coupled repression controls the level of transcriptional antagonism to PRC2 action. Thus, the effectiveness of this repression dictates the timescale for establishment of PRC2/H3K27me3 silencing. We experimentally validate these mechanistic model predictions, revealing that co-transcriptional processing sets the level of productive transcription at the locus, which then determines the rate of the ON-to-OFF switch to PRC2 silencing.
Collapse
Affiliation(s)
- Govind Menon
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Eduardo Mateo-Bonmati
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Robert Ietswaart
- Harvard Medical School, Department of Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| |
Collapse
|
5
|
Downie Ruiz Velasco A, Parsons AL, Heatley MC, Martin ARG, Smart AD, Shah N, Jopling CL. MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1. Nucleic Acids Res 2024:gkae505. [PMID: 38884273 DOI: 10.1093/nar/gkae505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/03/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024] Open
Abstract
In animals, microRNA (miRNA) biogenesis begins with cotranscriptional cleavage of the primary (pri-)miRNA by the Microprocessor complex. Cotranscriptional splicing has been shown to influence Microprocessor cleavage when miRNAs are hosted in introns of protein-coding pri-miRNAs, but the impact of splicing on production of miRNAs hosted in long non-coding (lnc)RNAs is largely unknown. Here, we investigated the role of splicing in the biogenesis of miR-122, an lncRNA-hosted, highly expressed, medically important, liver-specific miRNA. We found that splicing inhibition by the SF3B1 inhibitor pladienolide B (PlaB) led to strong and rapid reduction in transcription of endogenous, but not plasmid-encoded, pri-miR-122, resulting in reduced production of mature miR-122. To allow detection of rapid changes in miRNA biogenesis despite the high stability of mature miRNAs, we used SLAMseq to globally quantify the effects of short-term splicing inhibition on miRNA synthesis. We observed an overall decrease in biogenesis of mature miRNAs following PlaB treatment. Surprisingly, miRNAs hosted in exons and introns were similarly affected. Together, this study provides new insights into the emerging role of splicing in transcription, demonstrating novel biological importance in promotion of miR-122 biogenesis from an lncRNA, and shows that SF3B1 is important for global miRNA biogenesis.
Collapse
Affiliation(s)
| | - Aimee L Parsons
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Matthew C Heatley
- The Digital Research Service, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Athena R G Martin
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Alfredo D Smart
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Niraj Shah
- The Digital Research Service, University of Nottingham, Nottingham, NG7 2RD, UK
| | | |
Collapse
|
6
|
Li L, Zhang L, Luo L, Shen F, Zhao Y, Wu H, Huang Y, Hou R, Yue B, Zhang X. Adaptive Expression and ncRNA Regulation of Genes Related to Digestion and Metabolism in Stomach of Red Pandas during Suckling and Adult Periods. Animals (Basel) 2024; 14:1795. [PMID: 38929414 PMCID: PMC11200446 DOI: 10.3390/ani14121795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Red pandas evolved from carnivores to herbivores and are unique within Carnivora. Red pandas and carnivorous mammals consume milk during the suckling period, while they consume bamboo and meat during the adult period, respectively. Red pandas and carnivorous mammal ferrets have a close phylogenetic relationship. To further investigate the molecular mechanisms of dietary changes and nutrient utilization in red pandas from suckling to adult, comparative analysis of the whole transcriptome was performed on stomach tissues from red pandas and ferrets during the suckling and adult periods. The main results are as follows: (1) we identified ncRNAs for the first time in stomach tissues of both species, and found significant expression changes of 109 lncRNAs and 106 miRNAs in red pandas and 756 lncRNAs and 109 miRNAs in ferrets between the two periods; (2) up-regulated genes related to amino acid transport regulated by lncRNA-miRNA-mRNA networks may efficiently utilize limited bamboo amino acids in adult red pandas, while up-regulated genes related to amino acid degradation regulated by lncRNAs may maintain the balance of amino acid metabolism due to larger daily intakes in adult ferrets; and (3) some up-regulated genes related to lipid digestion may contribute to the utilization of rich nutrients in milk for the rapid growth and development of suckling red pandas, while up-regulated genes associated with linoleic acid metabolism regulated by lncRNA-miRNA-mRNA networks may promote cholesterol decomposition to reduce health risks for carnivorous adult ferrets. Collectively, our study offers evidence of gene expression adaptation and ncRNA regulation in response to specific dietary changes and nutrient utilization in red pandas during suckling and adult periods.
Collapse
Affiliation(s)
- Lu Li
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Liang Zhang
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (L.Z.); (F.S.); (R.H.)
| | - Lijun Luo
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (L.Z.); (F.S.); (R.H.)
| | - Yanni Zhao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611800, China; (H.W.); (Y.H.)
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611800, China; (H.W.); (Y.H.)
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (L.Z.); (F.S.); (R.H.)
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (L.L.); (L.L.); (Y.Z.); (B.Y.)
| |
Collapse
|
7
|
Han Z, Zhang L, Ma M, Keshavarzi M. Effects of MicroRNAs and Long Non-coding RNAs on Beneficial Action of Exercise on Cognition in Degenerative Diseases: A Review. Mol Neurobiol 2024:10.1007/s12035-024-04292-4. [PMID: 38869810 DOI: 10.1007/s12035-024-04292-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Recent research has exposed a growing body of proof underscoring the importance of microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) in maintaining the physical composition of neurons and influencing cognitive functioning in both standard and atypical circumstances. Extensive research has been conducted on the possible application of miRNAs and lncRNAs as biomarkers for various diseases, with a particular focus on brain disorders, as they possess remarkable durability in cell-free surroundings and can endure repeated freezing and thawing processes. It is intriguing to note that miRNAs and lncRNAs have the ability to function through paracrine mechanisms, thereby playing a role in communication between different organs. Recent research has proposed that the improvement of cognitive abilities through physical exercise in mentally healthy individuals is a valuable method for uncovering potential connections between miRNAs, or microRNAs, and lncRNAs, and human cognitive function. The process of cross-correlating data from disease models and patients with existing data will be crucial in identifying essential miRNAs and lncRNAs, which can potentially act as biomarkers or drug targets in the treatment of cognitive disorders. By combining this method with additional research in animal models, we can determine the function of these molecules and their potential impact on therapy. This article discusses the latest research about the primary miRNAs, lncRNAs, and their exosomes that are affected by physical activity in terms of human cognitive function.
Collapse
Affiliation(s)
- Zhen Han
- Department of Physical Education, Zhejiang International Studies University, Hangzhou, 310023, Zhejiang, China
| | - Lei Zhang
- Institute of Physical Education and Sports, Capital University Of Physical Education And Sports, Beijing, 100191, China.
| | - Minhang Ma
- Department of Physical Education, Zhejiang International Studies University, Hangzhou, 310023, Zhejiang, China
| | - Maryam Keshavarzi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
8
|
Ma X, He Y, Liu C, Zhu T, Li D, Li W, Sun G, Kang X. Long Noncoding RNA 6302 Regulates Chicken Preadipocyte Differentiation by Targeting SLC22A16. Genes (Basel) 2024; 15:758. [PMID: 38927694 PMCID: PMC11203196 DOI: 10.3390/genes15060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
The excessive deposition of abdominal adipocytes in chickens is detrimental to poultry production. However, the regulatory factors that affect abdominal adipogenesis in chickens are still poorly understood. SLC22A16 is differentially expressed in abdominal preadipocytes and 10-day differentiated adipocytes in chickens, but its role in regulating chicken adipogenesis has not been reported. In this study, the function of SLC22A16 in chicken abdominal preadipocytes was investigated. SLC22A16 is significantly upregulated during abdominal adipocyte differentiation. The overexpression of SLC2A16 upregulated the expression of adipogenic marker genes and proliferation-related genes, and promoted the proliferation of adipocytes and the accumulation of triglycerides. The knockdown of SLC22A16 downregulated the expression of adipogenic marker genes and proliferation-related genes, inhibited the proliferation of adipocytes, and impaired the accumulation of triglycerides in adipocytes. In addition, LNC6302 was differentially expressed in abdominal preadipocytes and mature adipocytes, and was significantly positively correlated with the expression of SLC22A16. Interference with LNC6302 inhibits the expression of adipogenic marker genes and proliferation-related genes. The data supported the notion that LNC6302 promotes the differentiation of chicken abdominal adipocytes by cis-regulating the expression of SLC22A16. This study identified the role of SLC22A16 in the differentiation and proliferation of chicken adipocytes, providing a potential target for improving abdominal adipogenesis in chickens.
Collapse
Affiliation(s)
- Xiangfei Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (X.M.); (Y.H.); (C.L.); (T.Z.); (D.L.); (W.L.)
| | - Yuehua He
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (X.M.); (Y.H.); (C.L.); (T.Z.); (D.L.); (W.L.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Cong Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (X.M.); (Y.H.); (C.L.); (T.Z.); (D.L.); (W.L.)
| | - Tingqi Zhu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (X.M.); (Y.H.); (C.L.); (T.Z.); (D.L.); (W.L.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (X.M.); (Y.H.); (C.L.); (T.Z.); (D.L.); (W.L.)
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (X.M.); (Y.H.); (C.L.); (T.Z.); (D.L.); (W.L.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Guirong Sun
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China; (X.M.); (Y.H.); (C.L.); (T.Z.); (D.L.); (W.L.)
| |
Collapse
|
9
|
Kim JM, Kim WR, Park EG, Lee DH, Lee YJ, Shin HJ, Jeong HS, Roh HY, Kim HS. Exploring the Regulatory Landscape of Dementia: Insights from Non-Coding RNAs. Int J Mol Sci 2024; 25:6190. [PMID: 38892378 PMCID: PMC11172830 DOI: 10.3390/ijms25116190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Dementia, a multifaceted neurological syndrome characterized by cognitive decline, poses significant challenges to daily functioning. The main causes of dementia, including Alzheimer's disease (AD), frontotemporal dementia (FTD), Lewy body dementia (LBD), and vascular dementia (VD), have different symptoms and etiologies. Genetic regulators, specifically non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are known to play important roles in dementia pathogenesis. MiRNAs, small non-coding RNAs, regulate gene expression by binding to the 3' untranslated regions of target messenger RNAs (mRNAs), while lncRNAs and circRNAs act as molecular sponges for miRNAs, thereby regulating gene expression. The emerging concept of competing endogenous RNA (ceRNA) interactions, involving lncRNAs and circRNAs as competitors for miRNA binding, has gained attention as potential biomarkers and therapeutic targets in dementia-related disorders. This review explores the regulatory roles of ncRNAs, particularly miRNAs, and the intricate dynamics of ceRNA interactions, providing insights into dementia pathogenesis and potential therapeutic avenues.
Collapse
Affiliation(s)
- Jung-min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyeon-su Jeong
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyun-Young Roh
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| |
Collapse
|
10
|
Ma RT, Wang Y, Ji F, Chen JN, Wang TJ, Liu Y, Hou MX, Guo ZG. YTHDF1's grip on CRC vasculature: insights into LINC01106 and miR-449b-5p-VEGFA axis. Cancer Cell Int 2024; 24:195. [PMID: 38835070 DOI: 10.1186/s12935-024-03360-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Investigating the unexplored territory of lncRNA m6A modification in colorectal cancer (CRC) vasculature, this study focuses on LINC01106 and YTHDF1. METHODS Clinical assessments reveal upregulated LINC01106 promoting vascular generation via the miR-449b-5p-VEGFA pathway. RESULTS YTHDF1, elevated in CRC tissues, emerges as an adverse prognostic factor. Functional experiments showcase YTHDF1's inhibitory effects on CRC cell dynamics. Mechanistically, Me-CLIP identifies m6A-modified LINC01106, validated as a YTHDF1 target through Me-RIP. CONCLUSIONS This study sheds light on the YTHDF1-mediated m6A modification of LINC01106, presenting it as a key player in suppressing CRC vascular generation.
Collapse
Affiliation(s)
- Rui-Ting Ma
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
- The Affiliated Hospital of Inner Mongolia Medical University, No.1, North Channel Road, Huimin District, Hohhot, 010050, China
| | - Yuanyuan Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Feng Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Jian-Nan Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
| | - Tian-Jun Wang
- Nanjing Medical University, Nanjing, Jiangsu, 210097, China
| | - Yan Liu
- The Affiliated Hospital of Inner Mongolia Medical University, No.1, North Channel Road, Huimin District, Hohhot, 010050, China
| | - Ming-Xing Hou
- The Affiliated Hospital of Inner Mongolia Medical University, No.1, North Channel Road, Huimin District, Hohhot, 010050, China.
| | - Zhi-Gang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.
- The Academy of Life Sciences, Nanjing Normal University, Nanjing, 210097, China.
| |
Collapse
|
11
|
Danga AK, Kour S, Kumari A, Rath PC. Cell-type specific and differential expression of LINC-RSAS long noncoding RNA declines in the testes during ageing of the rat. Biogerontology 2024; 25:543-566. [PMID: 38353919 DOI: 10.1007/s10522-023-10088-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/15/2023] [Indexed: 03/26/2024]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as major regulators of gene expression, chromatin structure, epigenetic changes, post-transcriptional processing of RNAs, translation of mRNAs into proteins as well as contributing to the process of ageing. Ageing is a universal, slow, progressive change in almost all physiological processes of organisms after attaining reproductive maturity and often associated with age-related diseases. Mammalian testes contain various cell-types, vast reservoir of transcriptome complexity, produce haploid male gametes for reproduction and testosterone for development and maintenance of male sexual characters as well as contribute genetic variation to the species. We report age-related decline in expression and cellular localization of Long intergenic noncoding repeat-rich sense-antisense (LINC-RSAS) RNA in the testes and its major cell-types such as primary spermatocytes, Leydig cells and Sertoli cells during ageing of the rat. LINC-RSAS expression in testes increased from immature (4-weeks) to adult (16- and 44-weeks) and declined from adult (44-weeks) to nearly-old (70-weeks) rats. Genomic DNA methylation in the testes showed a similar pattern. Cell-type specific higher expression of LINC-RSAS was observed in primary spermatocytes (pachytene cells), Leydig cells and Sertoli cells of testes of adult rats. Over-expression of LINC-RSAS in cultured human cell lines revealed its possible role in cell-cycle control and apoptosis. We propose that LINC-RSAS expression is involved in molecular physiology of primary spermatocytes, Leydig cells and Sertoli cells of adult testes and its decline is associated with diminishing function of testes during ageing of the rat.
Collapse
Affiliation(s)
- Ajay Kumar Danga
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15224, USA
| | - Anita Kumari
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
12
|
Yang F, Yan L, Ji J, Lou Y, Zhu J. HER2 puzzle pieces: Non-Coding RNAs as keys to mechanisms, chemoresistance, and clinical outcomes in Ovarian cancer. Pathol Res Pract 2024; 258:155335. [PMID: 38723327 DOI: 10.1016/j.prp.2024.155335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024]
Abstract
Ovarian cancer (OC) presents significant challenges, characterized by limited treatment options and therapy resistance often attributed to dysregulation of the HER2 signaling pathway. Non-coding RNAs (ncRNAs) have emerged as key players in regulating gene expression in OC. This comprehensive review underscores the pivotal role of ncRNAs in modulating HER2 signaling, with a specific focus on their mechanisms, impact on chemoresistance, and prognostic/diagnostic implications. MicroRNAs, long non-coding RNAs, and circular RNAs have been identified as essential regulators in the modulation of the HER2 pathway. By directly targeting key components of the HER2 axis, these ncRNAs influence its activation and downstream signaling cascades. Dysregulated ncRNAs have been closely associated with chemoresistance, leading to treatment failures and disease progression in OC. Furthermore, distinct expression profiles of ncRNAs hold promise as reliable prognostic and diagnostic markers, facilitating personalized treatment strategies and enhancing disease outcome assessments. A comprehensive understanding of how ncRNAs intricately modulate HER2 signaling is imperative for the development of targeted therapies and the improvement of patient outcomes. The integration of ncRNA profiles into clinical practice has the potential to enhance prognostic and diagnostic accuracy in the management of ovarian cancer. Further research efforts are essential to validate the clinical utility of ncRNAs and elucidate their precise roles in the regulation of HER2 signaling. In conclusion, ncRNAs play a crucial role in governing HER2 signaling in ovarian cancer, impacting chemoresistance and providing valuable prognostic and diagnostic insights. The exploration of ncRNA-mediated HER2 modulation offers promising avenues for the development of personalized treatment approaches, ultimately advancing patient care and outcomes in OC.
Collapse
Affiliation(s)
- Fangwei Yang
- Obstetrical Department, Yiwu Central Hospital, Yiwu, Zhejiang 322000, China.
| | - Lixiang Yan
- Obstetrical Department, Yiwu Central Hospital, Yiwu, Zhejiang 322000, China
| | - Junnan Ji
- Obstetrical Department, Yiwu Central Hospital, Yiwu, Zhejiang 322000, China
| | - Yunxia Lou
- Obstetrical Department, Yiwu Central Hospital, Yiwu, Zhejiang 322000, China
| | - Jinlu Zhu
- Obstetrical Department, Yiwu Central Hospital, Yiwu, Zhejiang 322000, China
| |
Collapse
|
13
|
Tashakori N, Kolour SSP, Ghafouri K, Ahmed SI, Kahrizi MS, Gerami R, Altafi M, Nazari A. Critical role of the long non-coding RNAs (lncRNAs) in radiotherapy (RT)-resistance of gastrointestinal (GI) cancer: Is there a way to defeat this resistance? Pathol Res Pract 2024; 258:155289. [PMID: 38703607 DOI: 10.1016/j.prp.2024.155289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 05/06/2024]
Abstract
Radiotherapy (RT) is a frequently used treatment for cervical cancer, effectively decreasing the likelihood of the disease returning in the same area and extending the lifespan of individuals with cervical cancer. Nevertheless, the primary reason for treatment failure in cancer patients is the cancer cells' resistance to radiation therapy (RT). Long non-coding RNAs (LncRNAs) are a subset of RNA molecules that do not code for proteins and are longer than 200 nucleotides. They have a significant impact on the regulation of gastrointestinal (GI) cancers biological processes. Recent research has shown that lncRNAs have a significant impact in controlling the responsiveness of GI cancer to radiation. This review provides a concise overview of the composition and operation of lncRNAs as well as the intricate molecular process behind radiosensitivity in GI cancer. Additionally, it compiles a comprehensive list of lncRNAs that are linked to radiosensitivity in such cancers. Furthermore, it delves into the potential practical implementation of these lncRNAs in modulating radiosensitivity in GI cancer.
Collapse
Affiliation(s)
- Nafiseh Tashakori
- Department of Internal Medicine, Faculty of Medicine, Tehran branch, Islamic Azad University, Tehran, Iran
| | | | - Kimia Ghafouri
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Sarah Ibrahem Ahmed
- Department of Anesthesia Techniques, Al-Noor University College, Nineveh, Iraq
| | | | - Reza Gerami
- Department of Radiology, Faculty of Medicine, AJA University of Medical Science, Tehran, Iran
| | - Mana Altafi
- Department of Radiology, Faculty of Biological Science and Technology, Shiraz Pardis Branch, Islamic Azad University, Shiraz, Iran.
| | - Afsaneh Nazari
- Department of Genetics, Faculty of Basic Sciences, Islamic Azad University, Zanjan Branch, Zanjan, Iran.
| |
Collapse
|
14
|
Sun G, Liu F, Lesany M, Nemati S. Comprehensive analysis of recently discovered lncRNA-associated competing endogenous RNA network in nasopharyngeal carcinoma. Pathol Res Pract 2024; 258:155314. [PMID: 38696855 DOI: 10.1016/j.prp.2024.155314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/04/2024]
Abstract
Nasopharyngeal carcinoma (NPC) arises from the epithelium of the nasopharynx and is characterized by geography-dependent incidence. Despite the high mortality rate, specifically in some ethnic groups, the mechanisms underlying NPC pathogenesis are not thoroughly understood and there is an urgent need to detect the potential and clinically applicable biomarkers to ameliorate the overall survival rate and improve the prognosis of patients. In recent years, research has increasingly focused on the importance of long non-coding RNAs (LncRNAs) in cancer progression. LncRNAs play critical roles in regulating gene expression through mechanisms such as competitively binding to microRNAs (CeRNA). While numerous LncRNAs have been studied in nasopharyngeal carcinoma (NPC), their potential as diagnostic and prognostic biomarkers have not been systematically examined. In the present study, we delve into elucidating the biological functions, molecular mechanisms, and clinical significance of newly identified LncRNAs that serve as sponges for different microRNAs in NPC. We highlight their regulatory mechanisms in promoting cell proliferation, invasion, and metastasis, and discuss their implications in diverse cancer-related signaling pathways. Our overall goal is to emboss the fundamental roles of LncRNA-mediated CeRNA networks in NPC progression, which may open up new avenues for determining the pathogenesis of NPC and developing effective prevention and treatment strategies.
Collapse
Affiliation(s)
- Guochen Sun
- Otolaryngology Department, Zhejiang Tongde Hospital, Hangzhou, Zhejiang 310000, China.
| | - Feng Liu
- Department of Stomatology, Zhejiang Province, Tongde Hospital, Hangzhou, Zhejiang 310000, China
| | - Maryam Lesany
- Department of Biology, Kavian Institute of Higher Education, Mashhad, Iran
| | - Sara Nemati
- Department of Medical sciences, Ardabil branch, Islamic Azad University, Ardabil, Iran
| |
Collapse
|
15
|
Ma K, Chu J, Liu Y, Sun L, Zhou S, Li X, Ji C, Zhang N, Guo X, Liang S, Cui T, Hu Q, Wang J, Liu Y, Liu L. Hepatocellular Carcinoma LINC01116 Outcompetes T Cells for Linoleic Acid and Accelerates Tumor Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400676. [PMID: 38460179 PMCID: PMC11151013 DOI: 10.1002/advs.202400676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Indexed: 03/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer with a highly immunosuppressive tumor microenvironment and a typical pattern of disturbances in hepatic lipid metabolism. Long non-coding RNAs are shown to play an important role in the regulation of gene expression, but much remains unknown between tumor microenvironment and lipid metabolism as a bridging molecule. Here, long intergenic nonprotein coding RNA 01116 (LINC01116) acts as this molecular which is frequently upregulated in HCC patients and associated with HCC progression in vitro and in vivo is identified. Mechanistically, LINC01116 stabilizes EWS RNA-binding protein 1 (EWSR1) by preventing RAD18 E3 Ubiquitin Protein Ligase (RAD18) -mediated ubiquitination. The enhanced EWSR1 protein upregulates peroxisome proliferator activated receptor alpha (PPARA) and fatty acid binding protein1 (FABP1) expression, a long-chain fatty acid (LCFA) transporter, and thus cancer cells outcompete T cells for LCFAs, especially linoleic acid, for seeding their own growth, leading to T cell malfunction and HCC malignant progression. In a preclinical animal model, the blockade of LINC01116 leads to enhanced efficacy of anti-PD1 treatment accompanied by increased cytotoxic T cell and decreased exhausted T cell infiltration. Collectively, LINC01116 is an immunometabolic lncRNA and the LINC01116-EWSR1-PPARA-FABP1 axis may be targetable for cancer immunotherapy.
Collapse
Affiliation(s)
- Kun Ma
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
| | - Junhui Chu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Yufeng Liu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Linmao Sun
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Shuo Zhou
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Xianying Li
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Changyong Ji
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Ning Zhang
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
| | - Xinyu Guo
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
| | - Shuhang Liang
- Department of Gastrointestinal SurgeryAnhui Province Key Laboratory of Hepatopancreatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
| | - Tianming Cui
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Qingsong Hu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Jiabei Wang
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Yao Liu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Lianxin Liu
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
| |
Collapse
|
16
|
Zhang A, Pi W, Wang Y, Li Y, Wang J, Liu S, Cui X, Liu H, Yao D, Zhao R. Update on functional analysis of long non-coding RNAs in common crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1389154. [PMID: 38872885 PMCID: PMC11169716 DOI: 10.3389/fpls.2024.1389154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.
Collapse
Affiliation(s)
- Aijing Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Wenxuan Pi
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yashuo Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuxin Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jiaxin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Shuying Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiyan Cui
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Huijing Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Rengui Zhao
- College of Agronomy, Jilin Agricultural University, Changchun, China
| |
Collapse
|
17
|
Cheng T, Gu ML, Xu WQ, Ye DW, Zha ZY, Fang WG, Mao LK, Ning J, Hu XB, Ding YH. Mechanism of lncRNA SNHG16 on kidney clear cell carcinoma cells by targeting miR-506-3p/ETS1/RAS/ERK molecular axis. Heliyon 2024; 10:e30388. [PMID: 38756581 PMCID: PMC11096951 DOI: 10.1016/j.heliyon.2024.e30388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Objective This study aimed to investigate the mechanism of long noncoding ribonucleic acid (lncRNA) SNHG16 on kidney clear cell carcinoma (KIRC) cells by targeting miR-506-3p/ETS proto-oncogene 1, transcription factor (ETS1)/RAS/Extracellular regulated protein kinases (ERK) molecular axis, thus to provide reference for clinical diagnosis and treatment of KIRC in the future. Methods Thirty-six patients with KIRC were enrolled in this study, and their carcinoma tissues and adjacent tissues were obtained for the detection of SNHG16/miR-506-3p/ETS1/RAS/ERK expression. Then, over-expressed SNHG16 plasmid and silenced plasmid were transfected into KIRC cells to observe the changes of their biological behavior. Results SNHG16 and ETS1 were highly expressed while miR-506- 3p was low expressed in KIRC tissues; the RAS/ERK signaling pathway was significantly activated in KIRC tissues (P < 0.05). After SNHG16 silence, KIRC cells showed decreased proliferation, invasion and migration capabilities and increased apoptosis rate; correspondingly, increase in SNHG16 expression achieved opposite results (P < 0.05). Finally, in the rescue experiment, the effects of elevated SNHG16 on KIRC cells were reversed by simultaneous increase in miR-506-3p, and the effects of miR-506-3p were reversed by ETS1. Activation of the RAS/ERK pathway had the same effect as increase in ETS1, which further worsened the malignancy of KIRC. After miR-506-3p increase and ETS1 silence, the RAS/ERK signaling pathway was inhibited (P < 0.05). At last, the rescue experiment (co-transfection) confirmed that the effect of SNHG16 on KIRC cells is achieved via the miR-506-3p/ETS1/RAS/ERK molecular axis. Conclusion SNHG16 regulates the biological behavior of KIRC cells by targeting the miR-506-3p/ETS1/RAS/ERK molecular axis.
Collapse
Affiliation(s)
- Tao Cheng
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Ming-Li Gu
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Wei-Qiang Xu
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Da-Wen Ye
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Ze-Yu Zha
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Wen-Ge Fang
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Li-Kai Mao
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Jing Ning
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Xing-Bang Hu
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| | - Yong-Hui Ding
- Department of Urology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, 233000, China
| |
Collapse
|
18
|
McShane A, Narayanan IV, Paulsen MT, Ashaka M, Blinkiewicz H, Yang NT, Magnuson B, Bedi K, Wilson TE, Ljungman M. Characterizing nascent transcription patterns of PROMPTs, eRNAs, and readthrough transcripts in the ENCODE4 deeply profiled cell lines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588612. [PMID: 38645116 PMCID: PMC11030308 DOI: 10.1101/2024.04.09.588612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Arising as co-products of canonical gene expression, transcription-associated lincRNAs, such as promoter upstream transcripts (PROMPTs), enhancer RNAs (eRNAs), and readthrough (RT) transcripts, are often regarded as byproducts of transcription, although they may be important for the expression of nearby genes. We identified regions of nascent expression of these lincRNA in 16 human cell lines using Bru-seq techniques, and found distinctly regulated patterns of PROMPT, eRNA, and RT transcription using the diverse biochemical approaches in the ENCODE4 deeply profiled cell lines collection. Transcription of these lincRNAs was influenced by sequence-specific features and the local or 3D chromatin landscape. However, these sequence and chromatin features do not describe the full spectrum of lincRNA expression variability we identify, highlighting the complexity of their regulation. This may suggest that transcription-associated lincRNAs are not merely byproducts, but rather that the transcript itself, or the act of its transcription, is important for genomic function.
Collapse
|
19
|
Orenay-Boyacioglu S, Dogan G, Caliskan M, Uzuner EG. Autoimmunity-related LINC01934 and AP002954.4 lncRNA polymorphisms may be effective in pediatric celiac disease: a case-control study. REVISTA DA ASSOCIACAO MEDICA BRASILEIRA (1992) 2024; 70:e20231490. [PMID: 38716950 PMCID: PMC11068376 DOI: 10.1590/1806-9282.20231490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/05/2023] [Indexed: 05/12/2024]
Abstract
OBJECTIVE Various studies have reported that certain long non-coding RNA levels are unusually low in the intestines of celiac disease patients, suggesting that this may be associated with the inflammation observed in celiac disease. Despite these studies, the research aimed at uncovering the potential role of long non-coding RNAs in the pathogenesis of autoimmune diseases like celiac disease remains insufficient. Therefore, in this study, we plan to assess long non-coding RNA polymorphisms associated with autoimmunity in children diagnosed with celiac disease according to the European Society for Paediatric Gastroenterology Hepatology and Nutrition criteria. METHODS DNA was isolated from paraffin tissue samples of 88 pediatric celiac disease patients and 74 healthy pediatric individuals. Single-nucleotide polymorphism genotyping of five long non-coding RNA polymorphisms associated with autoimmunity (LINC01934-rs1018326, IL18RAP-rs917997, AP002954.4-rs10892258, UQCRC2P1-rs6441961, and HCG14 rs3135316) was conducted using the TaqMan single-nucleotide polymorphism genotyping assays with the LightCycler 480. RESULTS In our study, the genotypic and allelic frequency distribution of LINC01934-rs1018326 and AP002954.4-rs10892258 polymorphisms was found to be statistically significant in the comparison between the two groups (p<0.05). According to the multiple genetic model analyses, the LINC01934-rs1018326 polymorphism was observed to confer a 1.14-fold risk in the recessive model and a 1.2-fold risk in the additive model for pediatric celiac disease. Similarly, the AP002954.4-rs10892258 polymorphism was found to pose a 1.40-fold risk in the dominant model and a 1.7-fold risk in the additive model. CONCLUSION Our study results draw attention to the LINC01934-rs1018326 and AP002954.4-rs10892258 polymorphisms in celiac disease and suggest that these polymorphisms may be associated with inflammation in autoimmune diseases like celiac disease.
Collapse
Affiliation(s)
- Seda Orenay-Boyacioglu
- Aydın Adnan Menderes University, Faculty of Medicine, Department of Medical Genetics, – Aydın, Turkey
| | - Guzide Dogan
- Haseki Education Research Hospital, Department of Pediatric Gastroenterology – İstanbul, Turkey
- Biruni University, Faculty of Medicine, Department of Pediatric Gastroenterology – İstanbul, Turkey
| | - Metin Caliskan
- Aydın Adnan Menderes University, Faculty of Medicine, Department of Medical Genetics, – Aydın, Turkey
- Uşak University, Faculty of Medicine, Department of Medical Biology – Uşak, Turkey
| | - Esen Gul Uzuner
- Haseki Education Research Hospital, Department of Pathology – İstanbul, Turkey
| |
Collapse
|
20
|
Huang P, Wen F, Li Y, Li Q. The tale of SOX2: Focusing on lncRNA regulation in cancer progression and therapy. Life Sci 2024; 344:122576. [PMID: 38492918 DOI: 10.1016/j.lfs.2024.122576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as influential contributors to diverse cellular processes, which regulate gene function and expression via multiple mechanistic pathways. Therefore, it is essential to exploit the structures and interactions of lncRNAs to comprehend their mechanistic functions within cells. A growing body of evidence has revealed that deregulated lncRNAs are involved in multiple regulations of malignant events including cell proliferation, growth, invasion, and metabolism. SRY-related high mobility group box (SOX)2, a well-recognized member of the SOX family, is commonly overexpressed in various types of cancer, contributing to tumor progression and maintenance of stemness. Emerging studies have shown that lncRNAs interact with SOX2 to remarkably contribute to carcinogenesis and disease states. This review elaborates on the crosstalk between the intricate and complicated functions of lncRNAs and SOX2 in the context of malignant diseases. We elucidate distinct molecular mechanisms that contribute to the onset/advancement of cancer, indicating that lncRNAs/SOX2 axes hold immense promise for potential therapeutic targets. Furthermore, we delve into the modalities of emerging feasible treatment options for targeting lncRNAs, highlighting the limitations of such therapies and providing novel insights into further ameliorations of targeted strategies of lncRNAs to promote the clinical implications. Translating current discoveries into clinical applications could ultimately boost improved survival and prognosis of cancer patients.
Collapse
Affiliation(s)
- Peng Huang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng Wen
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - YiShan Li
- Thoracic Oncology Ward, Cancer Center, West China Hospital, Sichuan University, West China School of Nursing, Chengdu, Sichuan 610041, China
| | - Qiu Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| |
Collapse
|
21
|
Chen X, Wang S, Jiang X, Zhang M, Ding Y. Long non-coding RNA HOTAIR: from pan-cancer analysis to colorectal cancer-related uridine metabolism. Aging (Albany NY) 2024; 16:7752-7773. [PMID: 38696320 PMCID: PMC11132002 DOI: 10.18632/aging.205781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/29/2024] [Indexed: 05/04/2024]
Abstract
Long non-coding RNAs (lncRNAs) are involved significantly in the development of human cancers. lncRNA HOTAIR has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. And it might have enormous potential to interpret the malignant progression of tumors in a broader perspective, that is, in pan-cancer. We comprehensively investigated the effect of HOTAIR expression on tumor prognosis across human malignancies by analyzing multiple cancer-related databases like The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER). Bioinformatics data indicated that HOTAIR was overexpressed in most of these human malignancies and was significantly associated with the prognosis of patients with cancer, especially in colorectal cancer (CRC). Subsequently, this study further clarified the utility of HOTAIR that downregulation of its expression could result in reduced proliferation and invasion of CRC cells. Mechanistically, HOTAIR upregulated the metabolic enzymes UPP1 by recruiting histone methyltransferase EZH2, thereby increasing the tumor progression. Our results highlight the essential role of HOTAIR in pan-cancer and uridine bypass, suggesting that the HOTAIR/EZH2/UPP1 axis might be a novel target for overcoming CRC. We anticipate that the role of HOTAIR in metabolism could be important in the context of CRC and even exploited for therapeutic purposes.
Collapse
Affiliation(s)
- Xuyu Chen
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Siying Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Jiang
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Min Zhang
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yanbing Ding
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| |
Collapse
|
22
|
Zhang J, Wu L, Wang C, Xie X, Han Y. Research Progress of Long Non-Coding RNA in Tumor Drug Resistance: A New Paradigm. Drug Des Devel Ther 2024; 18:1385-1398. [PMID: 38689609 PMCID: PMC11060174 DOI: 10.2147/dddt.s448707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/25/2024] [Indexed: 05/02/2024] Open
Abstract
In the past few decades, chemotherapy has been one of the most effective cancer treatment options. Drug resistance is currently one of the greatest obstacles to effective cancer treatment. Even though drug resistance mechanisms have been extensively investigated, they have not been fully elucidated. Recent genome-wide investigations have revealed the existence of a substantial quantity of long non-coding RNAs (lncRNAs) transcribed from the human genome, which actively participate in numerous biological processes, such as transcription, splicing, epigenetics, the cell cycle, cell differentiation, development, pluripotency, immune microenvironment. The abnormal expression of lncRNA is considered a contributing factor to the drug resistance. Furthermore, drug resistance may be influenced by genetic and epigenetic variations, as well as individual differences in patient treatment response, attributable to polymorphisms in metabolic enzyme genes. This review focuses on the mechanism of lncRNAs resistance to target drugs in the study of tumors with high mortality, aiming to establish a theoretical foundation for targeted therapy.
Collapse
Affiliation(s)
- Jing Zhang
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
| | - Le Wu
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
| | - Chenchen Wang
- Department of Critical Care Medicine, the 940th Hospital of Joint Logistics Support Force of PLA, Lanzhou, Gansu, People’s Republic of China
| | - Xin Xie
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
| | - Yuying Han
- Laboratory of Tissue Engineering, Faculty of Life Science, Northwest University, Xi’an, Shaanxi, People’s Republic of China
- Department of Critical Care Medicine, the 940th Hospital of Joint Logistics Support Force of PLA, Lanzhou, Gansu, People’s Republic of China
- Science and Education Department, Xi’an No. 5 Hospital, Xi’an, Shaanxi, People’s Republic of China
| |
Collapse
|
23
|
Hu Z, Yuan L, Yang X, Yi C, Lu J. The roles of long non-coding RNAs in ovarian cancer: from functions to therapeutic implications. Front Oncol 2024; 14:1332528. [PMID: 38725621 PMCID: PMC11079149 DOI: 10.3389/fonc.2024.1332528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/27/2024] [Indexed: 05/12/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are multifunctional and participate in a variety of biological processes and gene regulatory networks. The deregulation of lncRNAs has been extensively implicated in diverse human diseases, especially in cancers. Overwhelming evidence demonstrates that lncRNAs are essential to the pathophysiological processes of ovarian cancer (OC), acting as regulators involved in metastasis, cell death, chemoresistance, and tumor immunity. In this review, we illustrate the expanded functions of lncRNAs in the initiation and progression of OC and elaborate on the signaling pathways in which they pitch. Additionally, the potential clinical applications of lncRNAs as biomarkers in the diagnosis and treatment of OC were emphasized, cementing the bridge of communication between clinical practice and basic research.
Collapse
Affiliation(s)
- Zhong Hu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Lijin Yuan
- Department of Obstetrics and Gynecology, Huangshi Puren Hospital, Huangshi, Hubei, China
| | - Xiu Yang
- Department of Obstetrics and Gynecology, Huangshi Central Hospital, Huangshi, Hubei, China
| | - Cunjian Yi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Jinzhi Lu
- Department of Laboratory Medicine, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| |
Collapse
|
24
|
Song M, Wang H, Liu C, Jin S, Liu B, Sun W. Non-coding RNAs as regulators of the Hippo pathway in cardiac development and cardiovascular disease. Front Pharmacol 2024; 15:1348280. [PMID: 38698813 PMCID: PMC11063341 DOI: 10.3389/fphar.2024.1348280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
Cardiovascular diseases pose a serious threat to human health. The onset of cardiovascular diseases involves the comprehensive effects of multiple genes and environmental factors, and multiple signaling pathways are involved in regulating the occurrence and development of cardiovascular diseases. The Hippo pathway is a highly conserved signaling pathway involved in the regulation of cell proliferation, apoptosis, and differentiation. Recently, it has been widely studied in the fields of cardiovascular disease, cancer, and cell regeneration. Non-coding RNA (ncRNAs), which are important small molecules for the regulation of gene expression in cells, can directly target genes and have diverse regulatory functions. Recent studies have found that ncRNAs interact with Hippo pathway components to regulate myocardial fibrosis, cardiomyocyte proliferation, apoptosis, and hypertrophy and play an important role in cardiovascular disease. In this review, we describe the mode of action of ncRNAs in regulating the Hippo pathway, provide new ideas for further research, and identify molecules involved in the mechanism of action of ncRNAs and the Hippo pathway as potential therapeutic targets, with the aim of finding new modes of action for the treatment and prevention of cardiovascular diseases.
Collapse
Affiliation(s)
- Mengyang Song
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
| | - He Wang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
| | - Caixia Liu
- Department of Neurology, The Liaoning Province People’s Hospital, Shenyang, China
| | - Sijie Jin
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
| | - Wei Sun
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, China
| |
Collapse
|
25
|
Yu S, Cui X, Zhou S, Li Y, Feng W, Zhang X, Zhong Y, Zhang P. THOC7-AS1/OCT1/FSTL1 axis promotes EMT and serves as a therapeutic target in cutaneous squamous cell carcinoma. J Transl Med 2024; 22:347. [PMID: 38605354 PMCID: PMC11010364 DOI: 10.1186/s12967-024-05116-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND THOC7-AS1 and FSTL1 expression are frequently upregulated in cutaneous squamous cell carcinoma (cSCC). However, their molecular biological mechanisms remain elusive and their potential as therapeutic targets needs urgent exploration. METHODS Human tissue samples were used to evaluate clinical parameters. In vitro and in vivo experiments assessed biological functions. Quantitative PCR, western blot, immunohistochemistry, immunocytochemistry, immunoprecipitation, RNA fluorescence in situ hybridization, RNA pull-down, RNA immunoprecipitation, silver staining, chromatin immunoprecipitation, dual luciferase reporter assays etc. were utilized to explore the molecular biological mechanisms. RESULTS We found FSTL1 is an oncogene in cSCC, with high expression in tumor tissues and cells. Its elevated expression closely associates with tumor size and local tissue infiltration. In vitro and in vivo, high FSTL1 expression promotes cSCC proliferation, migration and invasion, facilitating malignant behaviors. Mechanistically, FSTL1 interacts with ZEB1 to promote epithelial-to-mesenchymal transition (EMT) in cSCC cells. Exploring upstream regulation, we found THOC7-AS1 can interact with OCT1, which binds the FSTL1 promoter region and promotes FSTL1 expression, facilitating cSCC progression. Finally, treating tumors with THOC7-AS1 antisense oligonucleotides inhibited cSCC proliferative and migratory abilities, delaying tumor progression. CONCLUSIONS The THOC7-AS1/OCT1/FSTL1 axis regulates EMT and promotes tumor progression in cSCC. This study provides clues and ideas for cSCC targeted therapy.
Collapse
Affiliation(s)
- Site Yu
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China
| | - Xu Cui
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China
| | - Situo Zhou
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China
| | - Yun Li
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China
| | - Wenjie Feng
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China
| | - Xiangjun Zhang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China
| | - Yuhui Zhong
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China
| | - Pihong Zhang
- Department of Burns and Plastic Surgery, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province, 410008, P.R. China.
| |
Collapse
|
26
|
Zhao K, Chen L, Xie Y, Ren N, Li J, Zhai X, Zheng S, Liu K, Wang C, Qiu Q, Peng X, Wang W, Liu J, Che Q, Fan J, Hu H, Liu M. m6A/HOXA10-AS/ITGA6 axis aggravates oxidative resistance and malignant progression of laryngeal squamous cell carcinoma through regulating Notch and Keap1/Nrf2 pathways. Cancer Lett 2024; 587:216735. [PMID: 38369001 DOI: 10.1016/j.canlet.2024.216735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 02/20/2024]
Abstract
As the second most prevalent malignant tumor of head and neck, laryngeal squamous cell carcinoma (LSCC) imposes a substantial health burden on patients worldwide. Within recent years, resistance to oxidative stress and N6-methyladenosine (m6A) of RNA have been proved to be significantly involved in tumorigenesis. In current study, we investigated the oncogenic role of m6A modified long non coding RNAs (lncRNAs), specifically HOXA10-AS, and its downstream signaling pathway in the regulation of oxidative resistance in LSCC. Bioinformatics analysis revealed that heightened expression of HOXA10-AS was associated with the poor prognosis in LSCC patients, and N (6)-Methyladenosine (m6A) methyltransferase-like 3 (METTL3) was identified as a factor in promoting m6A modification of HOXA10-AS and further intensify its RNA stability. Mechanistically, HOXA10-AS was found to play as a competitive endogenous RNA (ceRNA) by sequestering miR-29 b-3p and preventing its downregulation of Integrin subunit alpha 6 (ITGA6), ultimately enhancing the oxidative resistance of tumor cells and promoting the malignant progression of LSCC. Furthermore, our research elucidated the mechanism by which ITGA6 accelerates Keap1 proteasomal degradation via enhancing TRIM25 expression, leading to increased Nrf2 stability and exacerbating its aberrant activation. Additionally, we demonstrated that ITGA6 enhances γ-secretase-mediated Notch signaling activation, ultimately promoting RBPJ-induced TRIM25 transcription. The current study provides the evidence supporting the effect of m6A modified HOXA10-AS and its downstream miR-29 b-3p/ITGA6 axis on regulating oxidative resistance and malignant progression in LSCC through the Notch and Keap1/Nrf2 pathways, and proposed that targeting this axis holds promise as a potential therapeutic approach for treating LSCC.
Collapse
Affiliation(s)
- Kai Zhao
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Liwei Chen
- Department of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, PR China
| | - Yingli Xie
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China; Medical School of Chinese PLA, Beijing, 100853, PR China
| | - Nan Ren
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Jianhui Li
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Xingyou Zhai
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Shikang Zheng
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Kun Liu
- Department of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, PR China
| | - Cheng Wang
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Qibing Qiu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, PR China
| | - Xin Peng
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Wenjia Wang
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China; Medical School of Chinese PLA, Beijing, 100853, PR China
| | - Jinjing Liu
- Medical School of Chinese PLA, Beijing, 100853, PR China
| | - Qin Che
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Junda Fan
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China
| | - Hai Hu
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China.
| | - Mingbo Liu
- Department of Otolaryngology Head and Neck Surgery, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, PR China; Department of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Beijing 100853, PR China; The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, PR China.
| |
Collapse
|
27
|
Diao B, Luo J, Guo Y. A comprehensive survey on deep learning-based identification and predicting the interaction mechanism of long non-coding RNAs. Brief Funct Genomics 2024:elae010. [PMID: 38576205 DOI: 10.1093/bfgp/elae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/25/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) have been discovered to be extensively involved in eukaryotic epigenetic, transcriptional, and post-transcriptional regulatory processes with the advancements in sequencing technology and genomics research. Therefore, they play crucial roles in the body's normal physiology and various disease outcomes. Presently, numerous unknown lncRNA sequencing data require exploration. Establishing deep learning-based prediction models for lncRNAs provides valuable insights for researchers, substantially reducing time and costs associated with trial and error and facilitating the disease-relevant lncRNA identification for prognosis analysis and targeted drug development as the era of artificial intelligence progresses. However, most lncRNA-related researchers lack awareness of the latest advancements in deep learning models and model selection and application in functional research on lncRNAs. Thus, we elucidate the concept of deep learning models, explore several prevalent deep learning algorithms and their data preferences, conduct a comprehensive review of recent literature studies with exemplary predictive performance over the past 5 years in conjunction with diverse prediction functions, critically analyze and discuss the merits and limitations of current deep learning models and solutions, while also proposing prospects based on cutting-edge advancements in lncRNA research.
Collapse
Affiliation(s)
- Biyu Diao
- Department of Breast Surgery, The First Affiliated Hospital of Ningbo University, No. 59, Liuting Street, Haishu District, Ningbo 315000, China
| | - Jin Luo
- Department of Breast Surgery, The First Affiliated Hospital of Ningbo University, No. 59, Liuting Street, Haishu District, Ningbo 315000, China
| | - Yu Guo
- Department of Breast Surgery, The First Affiliated Hospital of Ningbo University, No. 59, Liuting Street, Haishu District, Ningbo 315000, China
| |
Collapse
|
28
|
Xia J, Huang Y, Ma M, Liu F, Cao B. Downregulating lncRNA MIAT attenuates apoptosis of podocytes exposed to high glucose. Acta Diabetol 2024; 61:451-460. [PMID: 38072843 DOI: 10.1007/s00592-023-02213-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/08/2023] [Indexed: 03/27/2024]
Abstract
AIMS Diabetic nephropathy (DN), a destructive complication of diabetes mellitus (DM), is one of the leading causes of end-stage renal disease (ESRD). This study aimed to investigate the role of long non-coding RNA (lncRNA) MIAT in high-glucose (HG)-induced podocyte injury associated with DN. METHODS Three human kidney podocyte (HKP) cultures were treated with HG to mimic DN. Expression of lncRNA MIAT, podocyte-specific and injury-related proteins, and apoptosis were assessed before and after MIAT knockdown using MIAT shRNAs. RESULTS MIAT expression was upregulated in HKPs in response to glucose stress. HG treatment resulted in a significant increase in the apoptotic rate, Bax level, and levels of injury-related proteins desmin, fibroblast-specific protein 1 (FSP-1), and smooth muscle α-actin (α-SMA), and a significant reduction in Bcl-2 levels and the levels of podocyte-specific proteins synaptopodin and podocin. Transfection of HKPs with shRNAs significantly reduced MIAT levels (p < 0.05) and attenuated apoptosis in HG-medium. Correspondingly, the levels of synaptopodin and podocin were upregulated, and desmin, FSP-1, and α-SMA were reduced (p < 0.05). Western blot analysis also showed that anti-apoptotic active caspase-3 and Bax and proapoptotic Bcl-2 were elevated and decreased, respectively, after MIAT knockdown, suggesting that apoptosis pathways are deactivated after MIAT downregulation. CONCLUSIONS High glucose upregulates MIAT level in HKPs and induces cellular injury. Knockdown of MIAT alleviates the injury likely via deactivating apoptosis pathways.
Collapse
Affiliation(s)
- Jiayi Xia
- Department of Endocrinology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550001, Guizhou, China
| | - Yan Huang
- Department of Medical Insurance, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550001, Guizhou, China
| | - Min Ma
- Department of Gynecology, Graduate School of Guizhou, University of Traditional Chinese Medicine, Guiyang, 550001, Guizhou, China
| | - Fang Liu
- Department of Coloproctology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550001, Guizhou, China.
| | - Bo Cao
- Department of Coloproctology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550001, Guizhou, China.
| |
Collapse
|
29
|
Abdullaev B, Alsaab HO, Hjazi A, Alkhafaji AT, Alawadi AH, Hamzah HF. The mechanisms behind the dual role of long non-coding RNA (lncRNA) metastasis suppressor-1 in human tumors: Shedding light on the molecular mechanisms. Pathol Res Pract 2024; 256:155189. [PMID: 38452581 DOI: 10.1016/j.prp.2024.155189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 03/09/2024]
Abstract
When the expression levels of metastasis suppressor-1 (MTSS1) were discovered to be downregulated in a metastatic cancer cell line in 2002, it was proposed that MTSS1 functioned as a suppressor of metastasis. The 755 amino acid long protein MTSS1 connects to actin and organizes the cytoskeleton. Its gene is located on human chromosome 8q24. The suppressor of metastasis in metastatic cancer was first found to be MTSS1. Subsequent reports revealed that MTSS1 is linked to the prevention of metastasis in a variety of cancer types, including hematopoietic cancers like diffuse large B cell lymphoma and esophageal, pancreatic, and stomach cancers. Remarkably, conflicting results have also been documented. For instance, it has been reported that MTSS1 expression levels are elevated in a subset of melanomas, hepatocellular carcinoma associated with hepatitis B, head and neck squamous cell carcinoma, and lung squamous cell carcinoma. This article provides an overview of the pathological effects of lncRNA MTSS1 dysregulation in cancer. In order to facilitate the development of MTSS1-based therapeutic targeting, we also shed light on the current understanding of MTS1.
Collapse
Affiliation(s)
- Bekhzod Abdullaev
- Research Department of Biotechnology, New Uzbekistan University, Mustaqillik Avenue 54, Tashkent 100007, Republic ofUzbekistan
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif 21944, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | | | - Ahmed Hussien Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Iraq
| | - Hamza Fadhel Hamzah
- Department of Medical Laboratories Technology, AL-Nisour University College, Baghdad, Iraq
| |
Collapse
|
30
|
Wang G, Lee-Yow Y, Chang HY. Approaches to probe and perturb long noncoding RNA functions in diseases. Curr Opin Genet Dev 2024; 85:102158. [PMID: 38412563 PMCID: PMC10987257 DOI: 10.1016/j.gde.2024.102158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 02/29/2024]
Abstract
Long noncoding RNAs (lncRNAs) are a class of RNA molecules exceeding 200 nucleotides in length that lack long open-reading frames. Transcribed predominantly by RNA polymerase II (>500nt), lncRNAs can undergo splicing and are produced from various regions of the genome, including intergenic regions, introns, and in antisense orientation to protein-coding genes. Aberrations in lncRNA expression or function have been associated with a wide variety of diseases, including cancer, cardiovascular diseases, diabetes, and neurodegeneration. Despite the growing recognition of select lncRNAs as key players in cellular processes and diseases, several challenges obscure a comprehensive understanding of their functional landscape. Recent technological innovations, such as in sequencing, affinity-based techniques, imaging, and RNA perturbation, have advanced functional characterization and mechanistic understanding of disease-associated lncRNAs.
Collapse
Affiliation(s)
- Guiping Wang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA. https://twitter.com/@Guiping_W
| | - Yannick Lee-Yow
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA. https://twitter.com/@yooaaooy
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
31
|
Ma F, Liu H, Xia T, Zhang Z, Ma S, Hao Y, Shen J, Jiang Y, Li N. HSFAS mediates fibroblast proliferation, migration, trans-differentiation and apoptosis in hypertrophic scars via interacting with ADAMTS8. Acta Biochim Biophys Sin (Shanghai) 2024; 56:440-451. [PMID: 38006215 PMCID: PMC10984868 DOI: 10.3724/abbs.2023274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Hypertrophic scar (HS) is one of the most common sequelae of patients, especially after burns and trauma. The roles of regulatory long noncoding RNAs (lncRNAs) in mediating HS remain underexplored. Human hypertrophic scar-derived fibroblasts (HSFBs) have been shown to exert more potent promoting effects on extracellular matrix (ECM) accumulation than normal skin-derived fibroblasts (NSFBs) and are associated with enhanced HS formation. The purpose of this study is to search for lncRNAs enriched in HSFBs and investigate their roles and mechanisms. LncRNA MSTRG.59347.16 is one of the most highly expressed lncRNAs in HS detected by lncRNA-seq and qRT-PCR and named as hypertrophic scar fibroblast-associated lncRNA (HSFAS). HSFAS overexpression significantly induces fibroblast proliferation, migration, and myofibroblast trans-differentiation and inhibits apoptosis in HSFBs, while knockdown of HSFAS results in augmented apoptosis and attenuated proliferation, migration, and myofibroblast trans-differentiation of HSFBs. Mechanistically, HSFAS suppresses the expression of A disintegrin and metalloproteinase with thrombospondin motifs 8 (ADAMTS8). ADAMTS8 knockdown rescues downregulated HSFAS-mediated fibroblast proliferation, migration, myofibroblast trans-differentiation and apoptosis. Thus, our findings uncover a previously unknown lncRNA-dependent regulatory pathway for fibroblast function. Targeted intervention in the HSFAS-ADAMTS8 pathway is a potential therapy for HS.
Collapse
Affiliation(s)
- Fang Ma
- School of Basic MedicineNingxia Medical UniversityYinchuan750004China
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
| | - Honglin Liu
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- Clinical Medical SchoolNingxia Medical UniversityYinchuan750004China
| | - Tongtong Xia
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
| | - Zhenghao Zhang
- School of Basic MedicineNingxia Medical UniversityYinchuan750004China
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
| | - Shengchao Ma
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
- Clinical Medical SchoolNingxia Medical UniversityYinchuan750004China
| | - Yinju Hao
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
| | - Jiangyong Shen
- General Hospital of Ningxia Medical UniversityYinchuan750004China
| | - Yideng Jiang
- School of Basic MedicineNingxia Medical UniversityYinchuan750004China
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
- Ningxia Key Laboratory of Vascular Injury and Repair ResearchNingxia Medical UniversityYinchuan750004China
| | - Nan Li
- NHC Key Laboratory of Metabolic Cardiovascular Diseases ResearchNingxia Medical UniversityYinchuan750004China
| |
Collapse
|
32
|
Dong J, Lv Y, Meng D, Shi R, Li F, Guo R, Wang Y, Guo J, Zhang Y. LncRNA WFDC21P interacts with SEC63 to promote gastric cancer malignant behaviors by regulating calcium homeostasis signaling pathway. Cancer Cell Int 2024; 24:111. [PMID: 38528582 DOI: 10.1186/s12935-024-03297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Gastric cancer is currently estimated to be the fifth leading common cancer in the world, and responsible for about one million new cases and an estimated 769,000 cancer-related deaths each year. WFDC21P is long non-coding RNA and has been reported to play critical roles in serval types of cancer. Our research aims to investigate the biological effects and molecular mechanism of WFDC21P in gastric cancer. METHODS Datasets (GSE53137, GSE58828, and GSE109476) in GEO database were used to screen differential expressed lncRNAs in gastric cancer by online GEO2R analysis tool. Quantitative RT-PCR was used to verify the above prediction in ten pairs of gastric cancer and corresponding paracancerous tissues. Pan-cancer analysis was used to analyze the expression of WFDC21P in different types of cancer. Small interfering RNAs were used to WFDC21P knockdown. CCK-8 and colony formation assays were used to measure the proliferation and tumorigenesis abilities. Wound healing and Transwell assay were used to detect the migration and invasion abilities. Proteins that interact with WFDC21P were predicted by catRAPID database. RNA pull down and RNA Immunoprecipitation were used to confirm the interaction. Western blotting was used to detect the key proteins level in calcium homeostasis signaling pathway. Loss-of-function and rescue assays were used to evaluate the biological function of SEC63 at the background of WFDC21P silencing. RESULTS WFDC21P was upregulated in gastric cancer tissues and cell lines. WFDC21P downregulation suppressed proliferation, tumorigenesis, migration, invasion, and promoted apoptosis in gastric cancer. SEC63 protein had the capability to bind with WFDC21P and the expression of SEC63 was regulated by WFDC21P. SEC63 was also upregulated in gastric cancer and exerted effects during tumor growth and metastasis. CONCLUSIONS This study confirmed that lncRNA WFDC21P aggravated gastric cancer malignant behaviors by interacting with SEC63 to regulate the calcium homeostasis signaling pathway.
Collapse
Affiliation(s)
- Jinyao Dong
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Yongqiang Lv
- Scientific Research Department, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, 030013, P. R. China
| | - Debin Meng
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Ruyi Shi
- Department of Cell biology and Genetics, Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China
| | - Feng Li
- Central Laboratory, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, 030013, P. R. China
| | - Rui Guo
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Yi Wang
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Jiansheng Guo
- Gastrointestinal Surgery Department, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China.
| | - Yanyan Zhang
- Hepatobiliary Pancreatic Surgery and Liver Transplantation Center, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China.
| |
Collapse
|
33
|
Caporali A, Anwar M, Devaux Y, Katare R, Martelli F, Srivastava PK, Pedrazzini T, Emanueli C. Non-coding RNAs as therapeutic targets and biomarkers in ischaemic heart disease. Nat Rev Cardiol 2024:10.1038/s41569-024-01001-5. [PMID: 38499868 DOI: 10.1038/s41569-024-01001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 03/20/2024]
Abstract
The adult heart is a complex, multicellular organ that is subjected to a series of regulatory stimuli and circuits and has poor reparative potential. Despite progress in our understanding of disease mechanisms and in the quality of health care, ischaemic heart disease remains the leading cause of death globally, owing to adverse cardiac remodelling, leading to ischaemic cardiomyopathy and heart failure. Therapeutic targets are urgently required for the protection and repair of the ischaemic heart. Moreover, personalized clinical biomarkers are necessary for clinical diagnosis, medical management and to inform the individual response to treatment. Non-coding RNAs (ncRNAs) deeply influence cardiovascular functions and contribute to communication between cells in the cardiac microenvironment and between the heart and other organs. As such, ncRNAs are candidates for translation into clinical practice. However, ncRNA biology has not yet been completely deciphered, given that classes and modes of action have emerged only in the past 5 years. In this Review, we discuss the latest discoveries from basic research on ncRNAs and highlight both the clinical value and the challenges underscoring the translation of these molecules as biomarkers and therapeutic regulators of the processes contributing to the initiation, progression and potentially the prevention or resolution of ischaemic heart disease and heart failure.
Collapse
Affiliation(s)
- Andrea Caporali
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Maryam Anwar
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Luxembourg, Luxemburg
| | - Rajesh Katare
- Department of Physiology, HeartOtago, University of Otago, Dunedin, New Zealand
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
| | | | - Thierry Pedrazzini
- Experimental Cardiology Unit, Division of Cardiology, Department of Cardiovascular Medicine, University of Lausanne Medical School, Lausanne, Switzerland
- School of Cardiovascular and Metabolic Medicine & Sciences, King's College London, London, UK
- British Heart Foundation Centre of Research Excellence, King's College London, London, UK
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, UK.
| |
Collapse
|
34
|
Yu X, Bu C, Yang X, Jiang W, He X, Sun R, Guo H, Shang L, Ou C. Exosomal non-coding RNAs in colorectal cancer metastasis. Clin Chim Acta 2024; 556:117849. [PMID: 38417779 DOI: 10.1016/j.cca.2024.117849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Colorectal cancer (CRC) is a type of gastrointestinal cancer with high morbidity and mortality rates, and is often accompanied by distant metastases. Metastasis is a major cause of shortened survival time and poor treatment outcomes for patients with CRC. However, the molecular mechanisms underlying the metastasis of CRC remain unclear. Exosomes are a class of small extracellular vesicles that originate from almost all human cells and can transmit biological information (e.g., nucleic acids, lipids, proteins, and metabolites) from secretory cells to target recipient cells. Recent studies have revealed that non-coding RNAs (ncRNAs) can be released by exosomes into the tumour microenvironment or specific tissues, and play a pivotal role in tumorigenesis by regulating a series of key molecules or signalling pathways, particularly those involved in tumour metastasis. Exosomal ncRNAs have potential as novel therapeutic targets for CRC metastasis, and can also be used as liquid biopsy biomarkers because of their specificity and sensitivity. Therefore, further investigations into the biological function and clinical value of exosomal ncRNAs will be of great value for the prevention, early diagnosis, and treatment of CRC metastasis.
Collapse
Affiliation(s)
- Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chiwen Bu
- Department of General Surgery, People's Hospital of Guanyun County, Lianyungang 222200, Jiangsu, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wenying Jiang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ru Sun
- Department of Blood Transfusion, Affiliated Hospital of North Sichuan Medical College, Xichang 637000, Sichuan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Li Shang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| |
Collapse
|
35
|
Talebi Taheri A, Golshadi Z, Zare H, Alinaghipour A, Faghihi Z, Dadgostar E, Tamtaji Z, Aschner M, Mirzaei H, Tamtaji OR, Nabavizadeh F. The Potential of Targeting Autophagy-Related Non-coding RNAs in the Treatment of Alzheimer's and Parkinson's Diseases. Cell Mol Neurobiol 2024; 44:28. [PMID: 38461204 PMCID: PMC10924707 DOI: 10.1007/s10571-024-01461-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024]
Abstract
Clearance of accumulated protein aggregates is one of the functions of autophagy. Recently, a clearer understanding of non-coding RNAs (ncRNAs) functions documented that ncRNAs have important roles in several biological processes associated with the development and progression of neurodegenerative disorders. Subtypes of ncRNA, including microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA), are commonly dysregulated in neurodegenerative disorders such as Alzheimer and Parkinson diseases. Dysregulation of these non-coding RNAs has been associated with inhibition or stimulation of autophagy. Decreased miR-124 led to decreased/increased autophagy in experimental model of Alzheimer and Parkinson diseases. Increased BACE1-AS showed enhanced autophagy in Alzheimer disease by targeting miR-214-3p, Beclin-1, LC3-I/LC3-II, p62, and ATG5. A significant increase in NEAT1led to stimulated autophagy in experimental model of PD by targeting PINK1, LC3-I, LC3-II, p62 and miR-374c-5p. In addition, increased BDNF-AS and SNHG1 decreased autophagy in MPTP-induced PD by targeting miR-125b-5p and miR-221/222, respectively. The upregulation of circNF1-419 and circSAMD4A resulted in an increased autophagy by regulating Dynamin-1 and miR-29c 3p, respectively. A detailed discussion of miRNAs, circRNAs, and lncRNAs in relation to their autophagy-related signaling pathways is presented in this study.
Collapse
Affiliation(s)
- Abdolkarim Talebi Taheri
- Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zakieh Golshadi
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Azam Alinaghipour
- School of Medical Sciences, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Zahra Faghihi
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
- Student Research Committee, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
| | - Zeinab Tamtaji
- Student Research Committee, Kashan University of Medical Sciences, Kashan, I.R. of Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. of Iran.
| | - Omid Reza Tamtaji
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
| | - Fatemeh Nabavizadeh
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
| |
Collapse
|
36
|
Hao Z, Jin X, Hickford JGH, Zhou H, Wang L, Wang J, Luo Y, Hu J, Liu X, Li S, Li M, Shi B, Ren C. Screening and identification of lncRNAs in preadipocyte differentiation in sheep. Sci Rep 2024; 14:5260. [PMID: 38438565 PMCID: PMC10912770 DOI: 10.1038/s41598-024-56091-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 03/01/2024] [Indexed: 03/06/2024] Open
Abstract
Studies of preadipocyte differentiation and fat deposition in sheep have mainly focused on functional genes, and with no emphasis placed on the role that long non-coding RNAs (lncRNAs) may have on the activity of those genes. Here, the expression profile of lncRNAs in ovine preadipocyte differentiation was investigated and the differentially expressed lncRNAs were screened on day 0 (D0), day 2(D2) and day 8(D8) of ovine preadipocyte differentiation, with their target genes being predicted. The competing endogenous RNA (ceRNA) regulatory network was constructed by GO and KEGG enrichment analysis for functional annotation, and some differentially expressed lncRNAs were randomly selected to verify the RNA-Seq results by RT-qPCR. In the study, a total of 2517 novel lncRNAs and 3943 known lncRNAs were identified from ovine preadipocytes at the three stages of differentiation, with the highest proportion being intergenic lncRNAs. A total of 3455 lncRNAs were expressed at all three stages of preadipocyte differentiation, while 214, 226 and 228 lncRNAs were uniquely expressed at day 0, day 2 and day 8, respectively. By comparing the expression of the lncRNAs between the three stages of differentiation stages, a total of 405, 272 and 359 differentially expressed lncRNAs were found in D0-vs-D2, D0-vs-D8, and D2-vs-D8, respectively. Functional analysis revealed that the differentially expressed lncRNAs were enriched in signaling pathways related to ovine preadipocyte differentiation, such as mitogen-activated protein kinase (MAPK) pathway, the phosphoinositide 3-kinase protein kinase B (PI3K-Akt) pathway, and the transforming growth factor beta (TGF-β) pathway. In summary, lncRNAs from preadipocytes at different stages of differentiation in sheep were identified and screened using RNA-Seq technology, and the regulatory mechanisms of lncRNAs in preadipocyte differentiation and lipid deposition were explored. This study provides a theoretical reference for revealing the roles of lncRNAs in ovine preadipocyte differentiation and also offers a theoretical basis for further understanding the regulatory mechanisms of ovine preadipocyte differentiation.
Collapse
Affiliation(s)
- Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiayang Jin
- Academic Animal & Veterinary Science, Qinghai University, Xining, China
| | - Jon G H Hickford
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Science, Lincoln University, Lincoln, 7647, New Zealand
| | - Huitong Zhou
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gene-Marker Laboratory, Faculty of Agriculture and Life Science, Lincoln University, Lincoln, 7647, New Zealand
| | - Longbin Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.
| | - Yuzhu Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Mingna Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bingang Shi
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Chunyan Ren
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
37
|
Xu Z, Nemati S. Long intergenic non-protein coding RNA 115 (Linc00115): A notable oncogene in human malignancies. Gene 2024; 897:148066. [PMID: 38070791 DOI: 10.1016/j.gene.2023.148066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Long noncoding RNAs (LncRNAs) are RNA transcripts ranging from 200 to 1000 nucleotides that have emerged as critical regulators of gene expression. Growing evidence highlights their involvement in tumor development. In particular, long intergenic non-protein coding RNA115 (Linc00115) has been identified as an oncogene across various human malignancies, with aberrant expression strongly linked to poor clinical outcomes in cancer patients. This review aims to delve into the expression patterns of Linc00115 and elucidate the underlying molecular mechanisms behind its oncogenic properties. Moreover, we discuss the potential utility of Linc00115 as a valuable diagnostic and prognostic biomarker in cancer.
Collapse
Affiliation(s)
- Zhujun Xu
- Wuhan No. 1 Hospital, Wuhan Hubei, 430022, China.
| | - Sara Nemati
- Department of Medical Sciences, Ardabil Branch, Islamic Azad University, Ardabil, Iran
| |
Collapse
|
38
|
Wang PS, Liu Z, Sweef O, Xie J, Chen J, Zhu H, Zeidler-Erdely PC, Yang C, Wang Z. Long noncoding RNA ABHD11-AS1 interacts with SART3 and regulates CD44 RNA alternative splicing to promote lung carcinogenesis. ENVIRONMENT INTERNATIONAL 2024; 185:108494. [PMID: 38364571 DOI: 10.1016/j.envint.2024.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Hexavalent chromium [Cr(VI)] is a common environmental pollutant and chronic exposure to Cr(VI) causes lung cancer in humans, however, the mechanism of Cr(VI) carcinogenesis has not been well understood. Lung cancer is the leading cause of cancer-related death, although the mechanisms of how lung cancer develops and progresses have been poorly understood. While long non-coding RNAs (lncRNAs) are found abnormally expressed in cancer, how dysregulated lncRNAs contribute to carcinogenesis remains largely unknown. The goal of this study is to investigate the mechanism of Cr(VI)-induced lung carcinogenesis focusing on the role of the lncRNA ABHD11 antisense RNA 1 (tail to tail) (ABHD11-AS1). It was found that the lncRNA ABHD11-AS1 expression levels are up-regulated in chronic Cr(VI) exposure-transformed human bronchial epithelial cells, chronically Cr(VI)-exposed mouse lung tissues, and human lung cancer cells as well. Bioinformatics analysis revealed that ABHD11-AS1 levels are up-regulated in lung adenocarcinomas (LUADs) tissues and associated with worse overall survival of LUAD patients but not in lung squamous cell carcinomas. It was further determined that up-regulation of ABHD11-AS1 expression plays an important role in chronic Cr(VI) exposure-induced cell malignant transformation and tumorigenesis, and the stemness of human lung cancer cells. Mechanistically, it was found that ABHD11-AS1 directly binds SART3 (spliceosome associated factor 3, U4/U6 recycling protein). The interaction of ABHD11-AS1 with SART3 promotes USP15 (ubiquitin specific peptidase 15) nuclear localization. Nuclear localized USP15 interacts with pre-mRNA processing factor 19 (PRPF19) to increase CD44 RNA alternative splicing activating β-catenin and enhancing cancer stemness. Together, these findings indicate that lncRNA ABHD11-AS1 interacts with SART3 and regulates CD44 RNA alternative splicing to promote cell malignant transformation and lung carcinogenesis.
Collapse
Affiliation(s)
- Po-Shun Wang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zulong Liu
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Osama Sweef
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jie Xie
- Department of Toxicology and Cancer Biology, University of Kentucky School of Medicine, Lexington, KY, USA
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, University of Kentucky School of Medicine, Lexington, KY, USA
| | - Haining Zhu
- Department of Biochemistry and Molecular Biology, University of Kentucky School of Medicine, Lexington, KY, USA
| | - Patti C Zeidler-Erdely
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV, USA
| | - Chengfeng Yang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Zhishan Wang
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA; Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
| |
Collapse
|
39
|
Al-Hawary SIS, Rodrigues P, Bangali H, Hassan ZF, Elawady A. The role of long noncoding RNA DGCR5 in cancers: Focus on molecular targets. Cell Biochem Funct 2024; 42:e3949. [PMID: 38379219 DOI: 10.1002/cbf.3949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/22/2024]
Abstract
Long noncoding RNAs (lncRNAs) are major components of cellular transcripts that are emerging as important players in various biological pathways. Due to their specific expression and functional diversity in a variety of cancers, lncRNAs have promising applications in cancer diagnosis, prognosis, and therapy. Studies have shown that lncRNA DiGeorge syndrome critical region gene 5 (DGCR5) with high specificity and accuracy has the potential to become biomarkers in cancers. LncRNA DGCR5 can be noninvasively extracted from body fluids, tissues, and cells, and can be used as independent or auxiliary biomarkers to improve the accuracy of diagnosis or prognosis. Now, the underlying mechanisms of lncRNAs such as DGCR5 were explored as therapeutic targets, which have been investigated in clinical trials of several cancers. The DGCR5 lacks an appropriate animal model, which is necessary to gain greater knowledge of their functions. While some studies on the uses of DGCR5 have been carried out, the small sample size makes them unreliable. In this review, we presented a compilation of recent publications addressing the potential of lncRNA DGCR5 that could be considered as biomarkers or therapeutic targets, with the hopes of providing promised implications for future cancer therapy.
Collapse
Affiliation(s)
| | - Paul Rodrigues
- Department of Computer Engineering, College of Computer Science, King Khalid University, Al-Faraa, Saudi Arabia
| | - Harun Bangali
- Department of Computer Engineering, College of Computer Science, King Khalid University, Al-Faraa, Saudi Arabia
| | | | - Ahmed Elawady
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, The Islamic University of Babylon, Babylon, Iraq
| |
Collapse
|
40
|
Liu C, Zhao X, Wang Z, Zhang C, Zheng W, Zhu X, Zhang D, Gong T, Zhao H, Li F, Guan T, Guo X, Zhang H, Yu B. LncRNA CHROMR/miR-27b-3p/MET axis promotes the proliferation, invasion, and contributes to rituximab resistance in diffuse large B-cell lymphoma. J Biol Chem 2024; 300:105762. [PMID: 38367665 PMCID: PMC10940993 DOI: 10.1016/j.jbc.2024.105762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/11/2024] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
Long non-coding RNAs (LncRNAs) could regulate chemoresistance through sponging microRNAs (miRNAs) and sequestering RNA binding proteins. However, the mechanism of lncRNAs in rituximab resistance in diffuse large B-cell lymphoma (DLBCL) is largely unknown. Here, we investigated the functions and molecular mechanisms of lncRNA CHROMR in DLBCL tumorigenesis and chemoresistance. LncRNA CHROMR is highly expressed in DLBCL tissues and cells. We examined the oncogenic functions of lncRNA CHROMR in DLBCL by a panel of gain-or-loss-of-function assays and in vitro experiments. LncRNA CHROMR suppression promotes CD20 transcription in DLBCL cells and inhibits rituximab resistance. RNA immunoprecipitation, RNA pull-down, and dual luciferase reporter assay reveal that lncRNA CHROMR sponges with miR-27b-3p to regulate mesenchymal-epithelial transition factor (MET) levels and Akt signaling in DLBCL cells. Targeting the lncRNA CHROMR/miR-27b-3p/MET axis reduces DLBCL tumorigenesis. Altogether, these findings provide a new regulatory model, lncRNA CHROMR/miR-27b-3p/MET, which can serve as a potential therapeutic target for DLBCL.
Collapse
MESH Headings
- Humans
- Carcinogenesis/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Gene Expression Regulation, Neoplastic
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Rituximab/pharmacology
- Rituximab/therapeutic use
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Drug Resistance, Neoplasm/genetics
- Antineoplastic Agents, Immunological/pharmacology
- Antineoplastic Agents, Immunological/therapeutic use
- Neoplasm Invasiveness
- Proto-Oncogene Proteins c-met/metabolism
Collapse
Affiliation(s)
- Chang Liu
- Department of Biochemistry and Molecular Biology, Changzhi Medical College, Changzhi, Shanxi, China; Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xinan Zhao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Zifeng Wang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Chan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China; Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Wenbin Zheng
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Xiaoxia Zhu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Dong Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Tao Gong
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Hong Zhao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China
| | - Feng Li
- Central Laboratory, Shanxi Cancer Hospital, Taiyuan, China; Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China; Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Tao Guan
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China; Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China; Department of Hematology, Shanxi Cancer Hospital, Taiyuan, China
| | - Xiangyang Guo
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China; Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China; Department of Breast Surgery, Shanxi Province Cancer Hospital, Taiyuan, China.
| | - Hongwei Zhang
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China; Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China; Department of Hematology, Shanxi Cancer Hospital, Taiyuan, China.
| | - Baofeng Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Medical University, Ministry of Education, Taiyuan, China.
| |
Collapse
|
41
|
Dong H, Sun Y, Nie L, Cui A, Zhao P, Leung WK, Wang Q. Metabolic memory: mechanisms and diseases. Signal Transduct Target Ther 2024; 9:38. [PMID: 38413567 PMCID: PMC10899265 DOI: 10.1038/s41392-024-01755-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Metabolic diseases and their complications impose health and economic burdens worldwide. Evidence from past experimental studies and clinical trials suggests our body may have the ability to remember the past metabolic environment, such as hyperglycemia or hyperlipidemia, thus leading to chronic inflammatory disorders and other diseases even after the elimination of these metabolic environments. The long-term effects of that aberrant metabolism on the body have been summarized as metabolic memory and are found to assume a crucial role in states of health and disease. Multiple molecular mechanisms collectively participate in metabolic memory management, resulting in different cellular alterations as well as tissue and organ dysfunctions, culminating in disease progression and even affecting offspring. The elucidation and expansion of the concept of metabolic memory provides more comprehensive insight into pathogenic mechanisms underlying metabolic diseases and complications and promises to be a new target in disease detection and management. Here, we retrace the history of relevant research on metabolic memory and summarize its salient characteristics. We provide a detailed discussion of the mechanisms by which metabolic memory may be involved in disease development at molecular, cellular, and organ levels, with emphasis on the impact of epigenetic modulations. Finally, we present some of the pivotal findings arguing in favor of targeting metabolic memory to develop therapeutic strategies for metabolic diseases and provide the latest reflections on the consequences of metabolic memory as well as their implications for human health and diseases.
Collapse
Affiliation(s)
- Hao Dong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuezhang Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lulingxiao Nie
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Aimin Cui
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Pengfei Zhao
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Wai Keung Leung
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Qi Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| |
Collapse
|
42
|
Wang A. Conceptual breakthroughs of the long noncoding RNA functional system and its endogenous regulatory role in the cancerous regime. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2024; 5:170-186. [PMID: 38464381 PMCID: PMC10918237 DOI: 10.37349/etat.2024.00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/18/2023] [Indexed: 03/12/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) derived from noncoding regions in the human genome were once regarded as junks with no biological significance, but recent studies have shown that these molecules are highly functional, prompting an explosion of studies on their biology. However, these recent efforts have only begun to recognize the biological significance of a small fraction (< 1%) of the lncRNAs. The basic concept of these lncRNA functions remains controversial. This controversy arises primarily from conventional biased observations based on limited datasets. Fortunately, emerging big data provides a promising path to circumvent conventional bias to understand an unbiased big picture of lncRNA biology and advance the fundamental principles of lncRNA biology. This review focuses on big data studies that break through the critical concepts of the lncRNA functional system and its endogenous regulatory roles in all cancers. lncRNAs have unique functional systems distinct from proteins, such as transcriptional initiation and regulation, and they abundantly interact with mitochondria and consume less energy. lncRNAs, rather than proteins as traditionally thought, function as the most critical endogenous regulators of all cancers. lncRNAs regulate the cancer regulatory regime by governing the endogenous regulatory network of all cancers. This is accomplished by dominating the regulatory network module and serving as a key hub and top inducer. These critical conceptual breakthroughs lay a blueprint for a comprehensive functional picture of the human genome. They also lay a blueprint for combating human diseases that are regulated by lncRNAs.
Collapse
Affiliation(s)
- Anyou Wang
- Feinstone Center for Genomic Research, University of Memphis, Memphis, TN 38152, USA
| |
Collapse
|
43
|
Wang X, Gu Y, Zhang L, Ma J, Xia Y, Wang X. Long noncoding RNAs regulate intrauterine adhesion and cervical cancer development and progression. Semin Cell Dev Biol 2024; 154:221-226. [PMID: 36841649 DOI: 10.1016/j.semcdb.2023.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/27/2023]
Abstract
Intrauterine adhesion, one of reproductive system diseases in females, is developed due to endometrial injury, such as infection, trauma, uterine congenital abnormalities and uterine curettage. Intrauterine adhesion affects female infertility and causes several complications, including amenorrhoea, hypomenorrhoea, and recurrent abortion. Cervical cancer is one of the common gynecological tumors and the fourth leading cancer-related death in women worldwide. Although the treatments of cervical cancer have been improved, the advanced cervical cancer patients have a low survival rate due to tumor recurrence and metastasis. The molecular mechanisms of intrauterine adhesion and cervical tumorigenesis have not been fully elucidated. In recent years, long noncoding RNAs (lncRNAs) have been known to participate in intrauterine adhesion and cervical carcinogenesis. Therefore, in this review, we will summarize the role of lncRNAs in regulation of intrauterine adhesion development and progression. Moreover, we will discuss the several lncRNAs in control of cervical oncogenesis and progression. Furthermore, we highlight that targeting lncRNAs could be used for treatment of intrauterine adhesion and cervical cancer.
Collapse
Affiliation(s)
- Xuemei Wang
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, China
| | - Yu Gu
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, China
| | - Leichao Zhang
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, China
| | - Jingchao Ma
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, China
| | - Yong Xia
- Department of Gynecology and Obstetrics, Fuzhou Maternity and Infant Hospital, Fuzhou, Fujian 350301, China
| | - Xueju Wang
- Department of Pathology, China-Japan Union Hospital, Jilin University, Changchun, Jilin 130033, China.
| |
Collapse
|
44
|
Peña-Flores JA, Muela-Campos D, Guzmán-Medrano R, Enríquez-Espinoza D, González-Alvarado K. Functional Relevance of Extracellular Vesicle-Derived Long Non-Coding and Circular RNAs in Cancer Angiogenesis. Noncoding RNA 2024; 10:12. [PMID: 38392967 PMCID: PMC10891584 DOI: 10.3390/ncrna10010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Extracellular vesicles (EVs) are defined as subcellular structures limited by a bilayer lipid membrane that function as important intercellular communication by transporting active biomolecules, such as proteins, amino acids, metabolites, and nucleic acids, including long non-coding RNAs (lncRNAs). These cargos can effectively be delivered to target cells and induce a highly variable response. LncRNAs are functional RNAs composed of at least 200 nucleotides that do not code for proteins. Nowadays, lncRNAs and circRNAs are known to play crucial roles in many biological processes, including a plethora of diseases including cancer. Growing evidence shows an active presence of lnc- and circRNAs in EVs, generating downstream responses that ultimately affect cancer progression by many mechanisms, including angiogenesis. Moreover, many studies have revealed that some tumor cells promote angiogenesis by secreting EVs, which endothelial cells can take up to induce new vessel formation. In this review, we aim to summarize the bioactive roles of EVs with lnc- and circRNAs as cargo and their effect on cancer angiogenesis. Also, we discuss future clinical strategies for cancer treatment based on current knowledge of circ- and lncRNA-EVs.
Collapse
Affiliation(s)
- José A. Peña-Flores
- Doctoral Program in Biomedical and Stomatological Sciences, Faculty of Dentistry, Autonomous University of Chihuahua, Chihuahua 31000, Mexico; (D.M.-C.); (R.G.-M.); (D.E.-E.); (K.G.-A.)
| | | | | | | | | |
Collapse
|
45
|
Chen X, Huang C, Zhang J, Hu Q, Wang D, You Q, Guo Y, Chen H, Xu J, Hu M. Mini crRNA-mediated CRISPR/Cas12a system (MCM-CRISPR/Cas12a) and its application in RNA detection. Talanta 2024; 268:125350. [PMID: 37922816 DOI: 10.1016/j.talanta.2023.125350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Some non-coding RNAs are abnormally expressed during the occurrence and development of diseases, so it is necessary to develop analytical methods that can specifically and sensitively detect them. In typical CRISPR/Cas12a system, a complete crRNA that can recognize single-stranded or double-stranded DNA is necessary to activate its trans-cleavage activity, which limits its direct application in RNA detection. Here, we prospectively find that slicing the facilitated crRNA in the typical CRISPR/Cas12a system at a fitted site did not affect its trans-cleavage activity, and a mini crRNA-mediated CRISPR/Cas12a system (MCM-CRISPR/Cas12a) was proposed based on this. This system can detect non-coding RNA to pM-level (10 pM for miRNA-21). To expand the application of this system, we combined it with HCR and CHA to establish a detection platform for non-coding RNA. The results show that the proposed method can specifically detect RNA to fM-level (2.5 fM for miRNA-21, 8.98 fM for miR-128-3p, and 81.6 fM for lncRNA PACER). The spiked recovery rates of miRNA-21, miR-128-3p, and lncRNA PACER in normal human serum were in range from 104.7 to 109.4 %, indicating the proposed method owns good applicability. In general, this MCM-CRISPR/Cas12a system further breaks the limitations of the typical CRISPR/Cas12a system that cannot be directly used for non-coding RNA detection. Besides, its combination with HCR and CHA achieves highly sensitive detection of non-coding RNA.
Collapse
Affiliation(s)
- Xiaolong Chen
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China.
| | - Chaowang Huang
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jing Zhang
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Qiao Hu
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Dan Wang
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Qianyi You
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Yawen Guo
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Huaping Chen
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Jing Xu
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China
| | - Mingdong Hu
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China; Department of Health Management, Xinqiao Hospital, Army Military Medical University, Chongqing, 400037, China.
| |
Collapse
|
46
|
Xiao S, Ouyang Q, Feng Y, Lu X, Han Y, Ren H, Huang Q, Zhao J, Xiao C, Yang M. LncNFYB promotes the proliferation of rheumatoid arthritis fibroblast-like synoviocytes via LncNFYB/ANXA2/ERK1/2 axis. J Biol Chem 2024; 300:105591. [PMID: 38141769 PMCID: PMC10867587 DOI: 10.1016/j.jbc.2023.105591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 12/25/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are specifically expressed in different diseases and regulate disease progression. To explore the functions of rheumatoid arthritis (RA)-specific lncRNA, we determined the lncRNA expression profile of fibroblast-like synoviocytes (FLS) obtained from patients with RA and osteoarthritis (OA) using a LncRNA microarray and identified up-regulated LncNFYB in RA as a potential therapeutic target. Using gain- and loss-of-function studies, LncNFYB was proven to promote FLS proliferation and cell cycle progress but not affect their invasion, migration, and apoptotic abilities. Further investigation discovered that LncRNA could combine with annexin A2 (ANXA2) and enhance the level of phospho-ANXA2 (Tyr24) in the plasma membrane area, which induced the activation of ERK1/2 to promote proliferation. These findings provide new insights into the biological functions of LncNFYB on modification of FLS, which may be exploited for the therapy of RA.
Collapse
Affiliation(s)
- Shibai Xiao
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qingqing Ouyang
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Feng
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoxi Lu
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yipeng Han
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hao Ren
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qin Huang
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinjun Zhao
- Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Changhong Xiao
- Department of Rheumatology and Immunology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China.
| | - Min Yang
- Nanfang Hospital, Southern Medical University, Guangzhou, China.
| |
Collapse
|
47
|
Zhang X, Li Y, Huan C, Hou Y, Liu R, Shi H, Zhang P, Zheng B, Wang Y, Wang H, Zhang W. LncRNA NKILA inhibits HBV replication by repressing NF-κB signalling activation. Virol Sin 2024; 39:44-55. [PMID: 37832719 PMCID: PMC10877346 DOI: 10.1016/j.virs.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023] Open
Abstract
Hepatitis B virus (HBV) infection results in liver cirrhosis and hepatocellular carcinoma (HCC). HBx/nuclear factor (NF)-κB pathway plays a role in HBV replication. However, whether NF-κB-interacting long noncoding RNA (NKILA), a suppressor of NF-κB activation, regulates HBV replication remains largely unknown. In this study, gain-and-loss experiments showed that NKILA inhibited HBV replication by inhibiting NF-κB activity. In turn, HBV infection down-regulated NKILA expression. In addition, expression levels of NKILA were lower in the peripheral blood-derived monocytes (PBMCs) of HBV-positive patients than in healthy individuals, which were correlated with HBV viral loads. And a negative correlation between NKILA expression level and HBV viral loads was observed in blood serum from HBV-positive patients. Lower levels of endogenous NKILA were also observed in HepG2 cells expressing a 1.3-fold HBV genome, HBV-infected HepG2-NTCP cells, stable HBV-producing HepG2.2.15 and HepAD38 cells, compared to those HBV-negative cells. Furthermore, HBx was required for NKILA-mediated inhibition on HBV replication. NKILA decreased HBx-induced NF-κB activation by interrupting the interaction between HBx and p65, whereas NKILA mutants lack of essential domains for NF-ĸB inhibition, lost the ability to inhibit HBV replication. Together, our data demonstrate that NKILA may serve as a suppressor of HBV replication via NF-ĸB signalling.
Collapse
Affiliation(s)
- Xi Zhang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China; Department of Ophthalmology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yuanyuan Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Chen Huan
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yubao Hou
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Rujia Liu
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Hongyun Shi
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Peng Zhang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China
| | - Baisong Zheng
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yingchao Wang
- Hepatobiliary Pancreatic Surgery, The First Hospital of Jilin University, Changchun, 130012, China.
| | - Hong Wang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China.
| | - Wenyan Zhang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130012, China; Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130012, China.
| |
Collapse
|
48
|
Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
Collapse
Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| |
Collapse
|
49
|
Hazazi A, AlShehah AA, Khan FR, Hakami MA, Almarshadi F, Abalkhail A, Nassar SA, Almasoudi HH, Ali AA, Abu-Alghayth MH, Kukreti N, Binshaya AS. From diagnosis to therapy: The transformative role of lncRNAs in eye cancer management. Pathol Res Pract 2024; 254:155081. [PMID: 38211388 DOI: 10.1016/j.prp.2023.155081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
The genomic era has brought about a transformative shift in our comprehension of cancer, unveiling the intricate molecular landscape underlying disease development. Eye cancers (ECs), encompassing diverse malignancies affecting ocular tissues, pose distinctive challenges in diagnosis and management. Long non-coding RNAs (lncRNAs), an emerging category of non-coding RNAs, are pivotal actors in the genomic intricacies of eye cancers. LncRNAs have garnered recognition for their multifaceted roles in gene expression regulation and influence on many cellular processes. Many studies support that the lncRNAs have a role in developing various cancers. Recent investigations have pinpointed specific lncRNAs associated with ECs, including retinoblastoma and uveal melanoma. These lncRNAs exert control over critical pathways governing tumor initiation, progression, and metastasis, endowing them with the ability to function as evaluation, predictive, and therapeutic indicators. The article aims to synthesize the existing information concerning the functions of lncRNAs in ECs, elucidating their regulatory mechanisms and clinical significance. By delving into the lncRNAs' expanding relevance in the modulation of oncogenic and tumor-suppressive networks, we gain a deeper understanding of the molecular complexities intrinsic to these diseases. In our exploration of the genomic intricacies of ECs, lncRNAs introduce a fresh perspective, providing an opportunity to function as clinical and therapeutic indicators, and they also have therapeutic benefits that show promise for advancing the treatment of ECs. This comprehensive review bridges the intricate relationship between lncRNAs and ECs within the context of the genomic era.
Collapse
Affiliation(s)
- Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | | | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Fahad Almarshadi
- Department of Public Health, College of Public Health and Health Informatics, University of Ha'il, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Qassim, Saudi Arabia
| | - Somia A Nassar
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia; Department of Parasitology & Animal Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Amer Al Ali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Mohammed H Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Abdulkarim S Binshaya
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
| |
Collapse
|
50
|
Jasim SA, Majeed AA, Uinarni H, Alshuhri M, Alzahrani AA, Ibrahim AA, Alawadi A, Abed Al-Abadi NK, Mustafa YF, Ahmed BA. Long non-coding RNA (lncRNA) PVT1 in drug resistance of cancers: Focus on pathological mechanisms. Pathol Res Pract 2024; 254:155119. [PMID: 38309019 DOI: 10.1016/j.prp.2024.155119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
According to estimates, cancer will be the leading cause of death globally in 2022, accounting for 9.6 million deaths. At present, the three main therapeutic modalities utilized to treat cancer are radiation therapy, chemotherapy, and surgery. However, during treatment, tumor cells resistant to chemotherapy may arise. Drug resistance remains a major oppose since it often leads to therapeutic failure. Furthermore, the term "acquired drug resistance" describes the situation where tumor cells already display drug resistance before undergoing chemotherapy. However, little is still known about the basic mechanisms underlying chemotherapy-induced drug resistance. The development of new technologies and bioinformatics has led to the discovery of additional genes associated with drug resistance. Long noncoding RNA plasmacytoma variant translocation 1 (PVT1) has been linked to an increased risk of cancer, according to a growing body of research. Apart from biological functions associated with cell division, development, pluripotency, and cell cycle, lncRNA PVT1 contributes significantly to the regulation of various aspects of genome function, such as transcription, splicing, and epigenetics. The article will address the mechanism by which lncRNA PVT1 influences drug resistance in cancer cells.
Collapse
Affiliation(s)
- Saade Abdalkareem Jasim
- Medical Laboratory Techniques Department, Al-maarif University College, Anbar, Iraq; Biotechnology department, College of Applied Science, Fallujah University, Anbar, Iraq
| | - Ali A Majeed
- Department of Pathological Analyses, Faculty of Science, University of Kufa, Najaf, Iraq.
| | - Herlina Uinarni
- Department of Anatomy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Indonesia; Radiology Department of Pantai Indah Kapuk Hospital, Jakarta, Indonesia.
| | - Mohammed Alshuhri
- Radiology and Medical Imaging Department, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Kharj, Sauadi Arabia
| | | | - Abeer A Ibrahim
- Inorganic Chemistry Group, Scientific Research Center, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Babylon, Iraq
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul 41001, Iraq
| | - Batool Ali Ahmed
- Department of Medical Engineering, Al-Nisour University College, Baghdad, Iraq
| |
Collapse
|